PDB 3Di Chains Dataset

Files

• 3di_chains_chaintag_filtered_prot_only.csv filtered out repeated protein and DNA RNA chain. Main file used for SFT
• _all contains all chains (including D-amino, RNA, DNA, and any others).
• _prot_only contains protein chains only (L- and D-amino acids treated as protein).
• _sample_1000 is a 1,000-row random sample for quick inspection.

Schema

• index — global row index from the source CSV (0-based)
• pdb_id — 4-character PDB code (e.g., 9B4J)
• chain_id — chain identifier (alphanumeric, may include digits/letters)
• aa_seq — amino-acid sequence (when available)
• threeDi_seq — Foldseek 3Di token sequence (Used for sft)
• combined_seq — helper concatenation (3Di/AA) used upstream
• seq_len — chain sequence length (prefer AA length; else derived)
• chunk — source folder name (e.g., 1000_1999)
• path — absolute path to the structure file used
• polymer_class — one of prot, DNA, RNA, other
  (D-amino peptides are classified as prot)

Basic Stats (from _all)